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gt-repfind - Online in the Cloud

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This is the command gt-repfind that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gt-repfind - Compute maximal exact matches (and more).

SYNOPSIS


gt repfind [options] -ii indexname

DESCRIPTION


-l [value]
Specify minimum length of matches (default: 0)

-f [yes|no]
Compute forward matches (default: yes)

-r [yes|no]
Compute reverse matches (default: no)

-p [yes|no]
Compute matches on reverse strand (default: no)

-seedlength [value]
Specify minimum length of seed (default: 0)

-maxfreq [value]
Specify maximal frequency of maximal exact matches in reference sequence (default: 0)

-extendxdrop [value]
Extend seed to both sides using xdrop algorithm, optional parameter specifies
sensitivity (default: 97)

-xdropbelow [value]
Specify xdrop cutoff score (argument 0 means undefined). If undefined an optimal value
is determined automatically depending on the error rate

-extendgreedy [value]
Extend seed to both sides using greedy algorithm with trimming of waves, optional
parameter specifies sensitivity (default: 97)

-minidentity [value]
Specify minimum identity of matches as integer in the range from 70 to 99 (for xdrop
and greedy extension) (default: 80)

-a [value]
show alignments/sequences for exact matches (optional argument is number of columns
per line) (default: 70)

-ii [string]
Specify input index (default: undefined)

-scan [yes|no]
scan index rather than map it to main memory (default: no)

-v [yes|no]
be verbose (default: no)

-help
display help and exit

-version
display version information and exit

REPORTING BUGS


Report bugs to <kurtz@zbh.uni-hamburg.de>.

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